KTIMPORTKRONA(1)

✨ NAME ✨

ktImportKrona — bestie, this is the one that lets you explore hierarchical metagenomic data with zoomable pie charts 💖 (section 1 of the manual, filed under User Commands, iykyk)

🌸 DESCRIPTION 🌸

Okay so here's the tea: ktImportKrona creates a Krona chart from the data in other Krona charts. Charts in, chart out. Iconic behavior honestly 🎀

💅 how you actually call it

ktImportKrona \
    [options] \
    krona_chart_1[:magnitudes_1][,name_1] \
    [krona_chart_2[:magnitudes_2][,name_2]] \
    ...

🦋 the arguments, explained with love

• krona_chart — a Krona HTML file that was created with KronaTools or the Krona Excel Template. By default, separate datasets will be created for each input (see [-c]). So yeah, one file in, one lil dataset out, unless you tell it otherwise 👑
• magnitudes — optional file listing query IDs with magnitudes, separated by tabs. This can be used to account for read length or contig depth to obtain a more accurate representation of abundance. By default, query sequences without specified magnitudes will be assigned a magnitude of 1. Magnitude files for assemblies in ACE format can be created with ktGetContigMagnitudes. Slay, accurate abundance ✨
• name — a name to show in the list of datasets in the Krona chart (this only matters if multiple input files are present and [-c] is not specified). By default, the basename of the file will be used. No name-picking stress required, it handles it 💖

💜 OPTIONS 💜

• -o <string> — output file name. [Default: 'krona.krona.html'] — yes, the default really is that gloriously redundant, we love her 🌈
• -n <string> — name of the highest level. Give your chart's top tier a title, main character energy 👑
• -c — combine data from each file, rather than creating separate datasets within the chart. One big beautiful dataset instead of a little collection 🫶
• -d <integer> — maximum depth of wedges to include in the chart. Depth check, literally 🌊
• -x <integer> — hue (0-360) for "bad" scores. Sad vibes get a color of your choosing 💀
• -y <integer> — hue (0-360) for "good" scores. Good vibes get a color too ⭐
• -u <string> — URL of Krona resources to use instead of bundling them with the chart (e.g. "http://krona.sourceforge.net"). Reduces size of charts and allows updates, though charts will not work without access to this URL.

🚨 bestie listen: it does shrink your charts and let you get updates, but if that URL isn't reachable, the chart is not working. No cap. Trade-off is real 😭

• -qp <string> — URL to send query IDs to (instead of listing them) for each wedge. The query IDs will be sent as a comma separated list in the POST variable "queries", with the current dataset index (from 0) in the POST variable "dataset". The url can include additional variables encoded via GET.

💖 okay this one is kinda the coolest: instead of dumping all the query IDs into the wedge, it POSTs them off somewhere. "queries" gets the comma separated list, "dataset" gets the dataset index counting from 0, and you can sneak extra GET variables into the url itself. iykyk 🌸

and that's the whole page, bestie!! 💅✨

this gorgeous little manual is for ktImportKrona version 2.8, dated June 2021 — shoutout to the KronaTools crew for feeding us, and that's a wrap 🎀🦋👑💜